[gmx-users] FeS4 cluster
spoel at xray.bmc.uu.se
Sat Dec 7 12:34:51 CET 2002
On Sat, 2002-12-07 at 13:03, Weihua Li wrote:
> >> Here's a sample:
> >> 5
> >> CYS SG 1 CYS SG 1 0.2 CYS2 CYS2
> >> You want to add
> >> Cys SG 1 FE FE 4 0.2 CYS1 FE
> >> What is the meaning of 4?
> that the FE can make 4 bonds.
> What about the case in the HEME Fe and S of Cys? 5,or 2?
> The value is 2 in the specbond.dat file.i don't know why? As you said,the value shoud be 5.
Chec your biochemistry textbook. There are different hemes around, the
iron has usually four bonds to nitrogens (these are not counted here
beacuse they are in the rtp file and should always be present in a
heme), but can have one or two to other ligands too.
Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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